Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp grompp gives following error.processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations
ERROR 1 [file seq.top, line 1965]: No default G96Bond types ERROR 2 [file seq.top, line 5271]: No default G96Angle types ERROR 3 [file seq.top, line 5272]: No default G96Angle types ERROR 4 [file seq.top, line 5648]: No default G96Angle types ERROR 5 [file seq.top, line 5653]: No default G96Angle types ERROR 6 [file seq.top, line 5654]: No default G96Angle types ERROR 7 [file seq.top, line 5655]: No default G96Angle types ERROR 8 [file seq.top, line 5656]: No default G96Angle types ERROR 9 [file seq.top, line 6201]: No default Proper Dih. types Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file seq.top, line 6932]: System has non-zero total charge: 7.000001e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note ------------------------------------------------------- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 9 errors in input file(s) ------------------------------------------------------- pdb2gmx works properly using ff43a1 forcefield. My protein contains Heme. This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of heme porphyrins. It is actually these six bond which is created in topology file with pdb2gmx using specbond.dat, giving error in grompp. I tried to find these bonds in in built files of gromacs i.e. /share/top/ but I couldnt. Can any one help me and tell me where can I find these bonds/angle parameters and what should I add in ffG43a1 .itp .rtp files please help. Shahid Nayeem
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